


New Beginnings

by afteriwake



Series: A New Life [1]
Category: Doctor Who, Sherlock (TV), Torchwood
Genre: Gen
Language: English
Status: Completed
Published: 2012-07-03
Updated: 2012-10-25
Packaged: 2017-11-09 03:22:16
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 2
Words: 5,138
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/450691
Author URL: https://archiveofourown.org/users/afteriwake/pseuds/afteriwake
Summary: <blockquote class="userstuff">
              <p>John Watson was just floating along in his life after Sherlock’s death, but Jack Harkness finds him and offers him the chance to give his life meaning again.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> I had planned on writing a short fic for the June Fanworks contest at [wholockians](http://wholockians.livejournal.com) but this idea struck and while I managed to get this all into one part I’m afraid it’s going to be another series. The second chapter was originally supposed to be the second story in the series, but I felt it worked better as the second half of this first story.

_Bring me home in a blinding dream_  
 _Through the secrets that I have seen_  
 _Wash the sorrow from off my skin_  
 _And show me how to be whole again_  
Linkin Park, “Castle Of Glass”

John was running. He was running towards the danger; after all, he was a doctor and a soldier, and both professions had drilled into him that he should save lives wherever possible. He was never one to shy away from a fight, and now that Sherlock wasn’t around he needed to do _something_ to fill the empty space. Taking the occasional case from Lestrade where his expertise could help was something, but it wasn’t enough. So he found himself keeping the peace in his area of London, stepping into things when they were small problems and keeping them from becoming worse.

Today it was a fight, right by his home. He could hear the shouting from his window, and saw the crowd gathering. It wasn’t the sort of problem he’d need to bring his gun for, so he’d made a dash out into the street. He got in the thick of the fight, quickly keeping it from escalating into a brawl, and managing to keep everyone involved safe and sound. When the crowd dispersed, he looked back to his home, but he had the feeling that not all of the crowd had left. He turned, and saw a man in a naval greatcoat, with a blue shirt and dark blue trousers on. “There’s nothing to see. Go on home,” he replied.

“There was a lot to see, Dr. Watson,” he said in an American accent with a grin on his face. “I’m almost disappointed it didn’t lead to violence. I wanted to see what you could do.”

John’s eyebrow rose slightly. A man who _wanted_ to see violence in a fight? Typical American, he thought to himself. “Look, I don’t know who you are, but I like to keep the peace around here. Any fight that ends without violence ends well, in my opinion.”

“Still, you’re a soldier. I mean, you were, but from my knowledge it’s once a soldier, always a soldier. You’re trained in, what, firearms and close combat?”

Now John just stared. “How did you know that? And for that matter, how did you know my name?”

“I should probably introduce myself,” the man said, coming closer. “Jack Harkness. Formerly of Torchwood Three.” Jack extended his hand. After a moment of John just staring at it, he lowered it. “You know, with Mycroft Holmes being an acquaintance I’m surprised it hasn’t been mentioned. He should have told you we’re trying to reopen the London office and we’re looking for good men.”

John didn’t tell him that he ignored all texts, calls and visits from Mycroft because it was never news he wanted to hear. Sherlock was gone, and anything that Mycroft had to say wouldn’t concern his brother, so he just ignored it. Maybe he shouldn’t have done that. “I’m sorry, but I’m not interested in a new job.”

“Maybe I should give old Mycroft a call,” Jack said. “I’m sure he can vouch for me. I’ve pulled his ass out of the fire a few times in the past.” He reached into his pocket and pulled out a cell phone. “Or do you want to just listen to what I have to say?”

“Call Mycroft,” John said.

Jack shrugged slightly, then hit a few buttons on the phone and put it to his ear. After a few moments he spoke. “Mycroft, this is Jack Harkness.” A brief pause. ”Yeah, yeah, I know, you never want to talk to me. I’m not bringing bad news. This time I just need your help—“ He paused again. “So, you don’t object? That’s good. You probably should have insisted on meeting with him face to face, though. I’ve got him here and he wanted me to call you.” There was another pause, a shorter one. “Wonderful.” Then Jack stepped closer and handed John his phone. “For you.”

John hesitantly took the phone and put it to his ear. “Hello?”

“I see Mr. Harkness tracked you down,” Mycroft said. “Listen to what he has to say. You could do a lot more good helping him then you would being a neighborhood watchmen.”

“Would Sherlock approve?” he asked, curious.

“Sherlock denies that what Jack does happens. He’s a skeptic. Even if he saw what Torchwood deals with face to face he would rationalize it, over analyze it and come up with some other reasoning for it. But yes, I believe he would approve.”

“What do you mean?” John asked.

“Just listen to Mr. Harkness and try to keep an open mind,” he replied. Then John heard the connection go dead on Mycroft’s side.

“So, what did good old Mycroft have to say?” Jack asked with a grin.

“He said I should listen to you and keep an open mind,” John said, handing him back his phone.

“Good man. I believe this is one less favor he owes me.” Jack pocketed his phone. “Let’s go sit and talk. I think you’ll find what I have to say to be…interesting…at any rate. And hopefully you’ll decide to help.”

“There’s a deli over there,” he replied, pointing to the deli next to 221 Baker Street.

“That’ll do,” Jack said with a nod. The two men headed over there, and the owner greeted John with a smile and asked if he wanted his usual. John shook his head, and then looked at Jack, who asked for a roast beef sandwich. After Jack got done paying the two men picked a seat in the back, away from the other customers. “I’m just going to come out and give you the honest truth about what Torchwood does. We deal with aliens, alien tech and work closely with UNIT and the British government,” he said quietly.

“Aliens?” John asked, his eyes wide. The only thing that kept him from bolting was that Mycroft had vouched for this man and he had already been warned to keep an open mind. But he could immediately see why Sherlock would never believe what they did. He had to admit it was strange to hear.

Jack nodded. “I used to run Torchwood Three, in Cardiff. I had a great team.” John was looking at him closely and could see his smile falter slightly. “I’m going to warn you that it’s a dangerous job. There’s no point in lying about that. I lost my old team to different things.”

“Lost? As in, they were killed?” John asked.

Jack nodded slowly. “The only one still alive is Gwen, and she doesn’t want to come on full time. She’s got a husband and a child. Wants to put them first, stay alive long enough to watch her child grow up. I can understand that. I have other recruits, people already familiar with at least one alien, but only a few of them are really trained in the more physical side of things. That’s why I could use you, to train them. Obviously you’d be doing more than that, but that’s how it would start.”

“Train them in what, exactly?”

“Weaponry, combat fighting, and things you learned in the army. Your medical skills would also be put to good use, though we do already have a medic with some combat training. Personally I doubt you’ll have to show Rory much of anything.”

“Rory?”

“One of the team members I already have. He spent two thousand years as a Roman centurion in another version of this universe, and he was a trained soldier in a third version. He remembers both timelines well enough, so he can draw on those experiences if needed. But in this universe he was a nurse.”

John narrowed his eyes. “More than one universe? Really?”

“There’s an alien known as The Doctor. He’s got a habit of picking up strays, making them his companions. I’m one of them, in his ninth and tenth regenerations. The other recruits were also companions. Martha Jones-Smith was a companion in his tenth regeneration, Mickey Smith was in the ninth and tenth, and Amy and Rory Williams were in the eleventh.” He stopped talking when his sandwich was brought to him. When the owner left he looked at John. “You can call Mycroft and he can tell you what the official files on these people say, if you’d rather believe him. Amy’s usually listed as Amelia in all the official stuff, and the Doctor refers to both of them as the Ponds.”

John stared slightly. “What happens if I don’t join?”

“I make you forget this conversation,” he replied before taking a bite of the sandwich. “It won’t hurt you, and you may remember later anyway. It’s not foolproof. I tell Mycroft you weren’t interested, and that’s the end of it.”

“Who suggested me?”

“Mycroft. I wasn’t looking for help, but he said you’d be good to add to the team. He seemed pretty insistent that I talk to you and extend an offer.”

John leaned back in the seat. “How long do I have to think it over?”

“Twenty-four hours.” Jack reached in his pocket and pulled out a card before handing it to John. “If you want to do this, just call that number. If I don’t hear from you by…” He checked his watch. “Five thirty tomorrow, I’ll come pay you a visit and get you to forget.” He took another bite of his sandwich. “Your choice, John. No pressure from me or from Mycroft, I promise.”

John fingered the card, then slipped it into his coat pocket. “I’ll think about it,” he said, standing up.

“Hope to hear from you soon,” Jack replied before taking another bite of his sandwich. John left him there, then went next door and went into the living room. He pulled his computer onto his lap after he sat down and began to research. There wasn’t much on Torchwood or on any of the names he had been given. 

Aliens. If he was entirely truthful with himself, he’d always suspected that they existed. He’d always wondered, at any rate. And in all honesty, there wasn’t much going for him now. He’d been in a haze of pain and grief when Sherlock killed himself, but he’d made the promise at his grave to soldier on, and he had. But this life wasn’t fulfilling. This life wasn’t even close to being a good enough reason to get out of bed in the morning.

He glanced over at the smiley face riddled with bullet holes, then at the other mementos and oddities that reminded him of his friend. He knew Sherlock had done it for what he considered to be good reasons. If there was any chance he was still alive, he knew that Sherlock would not want him to be wasting every day away on the trivial and unimportant things, the boring stuff he so detested. This new opportunity might not give him the thrill that working with Sherlock did, but it was probably better than his life now.

He glanced at the clock. It was only eight forty-seven. Perhaps if he slept on it, he might have a more concrete decision in the morning. He went to the kitchen, poured himself his customary nightcap, drank it, and then went to his room. He got ready for bed, then turned off the lights. But sleep did not come easily. He saw the pictures he’d seen online of the team members, his mind running through what he knew about each of them, and about the enigmatic Jack Harkness.

It was nearly six in the morning when he gave up trying to get a good night’s sleep. He went to his coat and pulled out the card, then went to his phone and dialed the number. It was picked up on the third ring. “Jack Harkness.”

“If I join Torchwood, do I need to give up consulting for DI Lestrade? Or my patients at the clinic?”

“No to Lestrade, but yes to the clinic. I mean, hypothetically, you could put in a couple days here and there, but there are more alien interactions than you could possibly dream of.”

“Can you guarantee the safety of my friends?”

“What, you mean like the threat Moriarty posed?” John was surprised he knew that. “I can’t guarantee anything like that, but I can promise we will try and minimize how much your job would affect them.”

“One last question.”

“Sure.”

“Would I still be allowed to continue my search for clues that Sherlock Holmes is still alive?”

There was a pause. “Not only can you do that, I’ll help.”

That surprised John even more than his knowledge of the threat Moriarty had posed. “You will?”

“Look, I know what it’s like to have your world flipped upside down by something like that. If it’s important to you that you try and find him, I can give you resources you can’t even imagine. But I’m going to ask for a promise in exchange.”

“All right.”

“If you don’t find the information you need in six months, you stop looking. I know you’ve spent the last eighteen months searching. Six months with my resources will either yield results or you’ll have to admit he’s really dead. Can you agree to that?”

“Yes,” John replied. He knew Mycroft and Mrs. Hudson and Lestrade and even Molly wanted him to stop. If he could get extra help now he’d give up in six months if no sign of him was found. Six months was long enough. “Yes, I will stop looking if we don’t find him in six months.”

“All right then. John Watson, welcome to Torchwood. Everyone will be at the office in a couple hours. Go to the address I’m about to give you at nine sharp.”

“Do I need to bring anything with me? Do I need to dress any certain way?”

“Nope. I mean, don’t come in your pajamas, but it’s not fancy. Be comfortable, though. I’m throwing you headfirst into the training today. Got a pen?”

John went to his desk and grabbed one, and pulled up his notepad. “Yes.” Jack rattled off an address, and John wrote it down. “I’ll be waiting outside. See you at nine.”

Jack hung up first, and once John had put the phone down he picked up the notepad. This was definitely going to be an interesting day, and he knew he needed to steel himself for anything. With that thought in mind, he began to get ready. He might as well make a good first impression to everyone except Jack.


	2. Chapter 2

John got out of the cab after it had pulled up to the building. It was a nondescript building, nothing special about it. He double checked the address to make sure he was at the right place. There wasn’t a door facing the street, so he went around to the alley, finding a green door on the side. He knocked, and then waited.

A small panel in the door opened, and he saw a set of eyes looking at him. “Name?” a female voice asked.

“John Watson,” he said.

The panel closed and the door opened, and a woman with a smile on her face stood there. She had brilliant red hair and he recognized her as Amy Pond. He looked at her more closely. She was in blue jean pants and a green plaid shirt with black boots on. “Good to know you didn’t get lost. Come on in, John. Everyone else is already here.” She turned and walked down a hallway, and he followed. “Sorry Jack wasn't outside. He had something to attend to, and it was my day to watch the door, which is rather nice because we’re really excited that you decided to join. Rory didn’t think you’d do it. He owes me an expensive Italian dinner now.”

“I’m still not a hundred percent sure,” John said as they headed down a flight of stairs to another door. There was an optical scanner and a press pad on it. Amy stood and let it scan her eyes while she put her palm on the reader. The door clicked open and she pushed it. The area they walked into was much larger than the building should be, and was filled with high tech equipment. He saw Jack there, and the other people he had only seen pictures of: Rory Williams, Martha Smith-Jones and Mickey Smith. There was also a woman with frizzy blonde hair who he did not recognize.

“Hey, John,” Jack said with a wide grin. “Welcome to Torchwood. Guess we should get the introductions over with. This guy to my left is Rory Williams, the guy to my right is Mickey Smith, the woman in front of him is Martha Smith-Jones, and the dashing woman behind me is River Song.”

The others waved and said hello. River was the only one to come up to him, offering her hand. “I’ve read a lot about you, Doctor Watson. It’s a pleasure to finally meet the legend in person.”

“Legend?” John asked, shaking her hand. “I’m no legend.”

“The faithful blogger? The one who searched for Sherlock Holmes for years, brought a good man back to the world?”

John’s eyes widened. “How…?”

“River usually resides in the 51sy century,” Jack said with a grin. “She’s an archaeologist.” 

“I’m also a part time associate of Torchwood, just like my husband is a part time associate of UNIT,” she said with a chuckle. “Of course, it helps that my mum and dad are Torchwood members.”

“River,” Rory said, shaking his head. “I thought you weren’t dropping that bombshell on everyone you meet when you meet them.”

“Sorry, Dad,” she said with a chuckle. He could tell his eyes were wide because when she turned back to him she laughed a full blown laugh. “As my husband likes to say wibbly wobbly timey wimey stuff. Amy and Rory are my mum and dad, only they didn’t get to raise me. And, in case you’re wondering my husband is their friend, the Doctor. That’s also somewhat complicated, seeing as how we got married when all of time was happening at once.”

“I don’t…” John began but then shook his head. “I suppose I’ll learn.”

“River’s just a tease,” Jack replied. “Which is probably why I like her so much, and also why I’m incredibly jealous.”

“He had to settle down again eventually, dear, and you’re just not his type,” River said sweetly as she turned to him. “Which is rather a shame. We could have had some fun together.”

“River,” Rory said, blushing slightly.

“Didn’t mean to embarrass you, Dad,” she said, going over to him to give him a hug. “Well, I made my introductions so I’m off. You have all the information I have on Sherlock Holmes. There aren’t a whole lot of specific dates because no biographer talked about this period of his life, but there might be clues. I don’t know exactly when you find him John, but I hope it’s soon.” She walked over to Amy and gave her a hug. “Good-bye, Mum. I’ll see you for dinner next week.”

“Bye, sweetie,” Amy said, hugging River back. When River let go she lifted up her wrist touched a few buttons on the device on it and then was gone. Amy turned back to John at that point. “I swear, it’s really not that confusing. And we are actually much more normal than you’d imagine.”

“As I said before I guess I’ll learn,” John said with a slight nod.

“That’s the best attitude to have,” John said with a grin. “Mickey, why don’t you take John on the tour? Let him get the lay of the land.”

“Right,” Mickey said with a grin. He stood up and went over to John. “Come on, there’s a lot to see.” He then walked out of the main room and John followed. It seemed as though the tour was going to take a while; he showed him where the labs were, and the armory and the communications center, and where they kept the alien tech they found that wasn’t weaponry. John stayed silent through most of it, making the occasional vague comment. Finally they got to the area where aliens were held. “We actually have on in here,” he said. “It’s not harmful, not really. We’re just waiting for it to be picked up by the rest of its race. It’s telepathic but if it communicates with the wrong people it can give someone a waking nightmare.”

“How do you know if you’re the wrong person?” John asked intrigued.

“You don’t, until it tries to communicate with you. Martha can’t be in the same room as it, but the rest of us are fine.”

“I’d like to see it if that’s all right.”

Mickey looked unsure for a moment. “It takes a few minutes to wake up from the nightmare, if it puts you in one.”

“That’s all right,” John said.

Mickey nodded, and opened up the door. They walked inside and John saw a bunch of areas that looked like jail cells, though they didn’t have metal bars instead being protected by something that looked like clear plastic tubing that was filled with energy. Mickey led him to the one farthest away from the door and he looked in The alien was human shaped but his skin seemed to be an iridescent color that changed as it moved. It came over to the bars, careful not to touch them. “Here it is.”

John felt something in his head, a light touch. And then the alien was talking through images, and John could see it all. He thought of responses and the alien replied back with more images. It went on like this for about ten minutes before he felt the presence in his mind leave. He felt himself grin slightly. He’d actually communicated with a real live alien. This…this was interesting. “I think he’s done talking to me,” he said as the alien went back to the seat in the room.

“Longest he’s talked to any of us. Jack will want to know what he said,” Mickey said. “Come on let’s get back to him.” They left then and began the walk back. “Not all of the aliens are harmless,” Mickey said. “That one is more the exception than the rule.”

“Ah,” John said. “Have you dealt with any hostile aliens?”

“A few. Some with the Doctor, but most of them when I worked with UNIT and here.” Mickey shrugged slightly. “You get used to it.”

“I hope I can get used to it,” John said. “I need to do something more than I do now. I’m just not living, the way I am right now.”

“This will change you, mate,” Mickey said. “I just hope you’re ready for it.”

“I guess I have to be,” he replied. They made their way back in silence, and when they got back to the main room Jack wasn’t there but there was food waiting for them. “Smells like a bakery in here,” he said.

“Didn’t know what you’d like so we ordered a bit extra of everything,” Amy said with a nod. “Bagels, pastries, even croissants. Go ahead and dig in.”

“Where’s Jack?” he asked, picking up a croissant.

“Had to take care of an errand,” Rory said. “He said he’ll be back soon.” He had been eating a bagel. “What did you think?”

“It’s all very impressive,” he said with a nod. “A lot of it I don’t understand, but I expect I’ll learn eventually.”

“We’ll be glad to teach you,” Martha said with a smile. “And I expect there’s a lot you can teach us. I mean, I have no training as a combat medic. Regular doctor, yes, but not that.”

“Same here,” Rory said. “I can do it if I have the right supplies, but I was trained as a nurse, not a doctor. I’m more support than anything else.”

“Yeah, but you have all that Roman soldier training in your head,” Mickey pointed out. “You know how to use practically any weapon made in the last two thousand years, and use it well.”

Rory shrugged slightly. “It’s what I get for being made of plastic. Had to do something to keep Amy safe.” He glanced over at John, who must have looked confused, because he grinned slightly. “It’s a long story, which I’ll go into sometime. I promise.”

“I think I’d like to hear it,” John said with a nod.

“Just remember to set aside an entire evening for it,” Amy said with a smile. “It’s long, but trust me when I say it’s not boring.”

The door opened up again and Jack came back in. “Enjoy the tour?” he asked John.

John nodded. “Yeah. It was informative.”

“Excellent!” Jack said. “We’ll get to work later this afternoon, then. See if you can start doing some of the training, learning some of the weapons we use here.” He looked around at the food and went to go get a bagel. “Have any cream cheese?”

Martha pointed to a container next to Mickey. “Over there.”

Jack went over to it, picking it and the knife that was I it up. He spread some on his bagel and took a bite. “This would be better with lox,” he said after a moment.

“Yeah, well, I forgot,” Amy said, shaking her head. She took a bite of her Danish. “Do I need to go back to the door?”

“Nope. It’s Martha’s turn now, at least until I start having John go over combat medical training. I figured Rory could show him around the armory, get him comfortable there. You could always use some extra training so I thought you might want to tag along.”

“All right,” Amy said with a nod as Martha got up and headed back where Jack had come from. “Come on, boys. Leave the food behind.”

John set down the rest of his croissant as Rory finished his last bite, and they followed Amy to the armory. Rory opened the weapons cabinet Mickey had shown him earlier and looked at it, pulling out a .45. “We’ll start with regular weapons first. This looks like it will be a good fit for you. John.” He handed it to John, then pulled out some bullets, followed by ear protectors. “Here you go.”

John put the protectors on, then took the gun and the bullets and loaded the gun. Rory put a target up and sent it back a ways. John took aim and shot at the target as Rory got Amy ready. He sent Amy’s target back before bringing up John’s. All but one shot landed in the center of the head, the stray one going off towards where his ear would be. “That one shot would have turned him into van Gogh,” John mused.

“Vincent was a nice man,” Amy said before shooting at her target. When she was done she pulled her protector off. “Of course, I met him before he cut his ear off.”

“You really met Vincent van Gogh?” John asked surprised.

Amy nodded. “Yup. Inspired him to paint all those sunflower paintings by filling up his courtyard with the flowers. It took me two hours to get them all cut down and in place. But the art was worth it.” She smiled. “One of his painting is even dedicated to me.”

“That’s fascinating,” John said, slightly in awe.

“We’ve met loads of people,” Rory said as he brought her target closer. “So has Martha. Mickey not as much. Jack, though…Jack beats us all.” He pulled her target off when it got close enough. “You’re getting better, Amy.”

“Good. I’ve been practicing when I get the chance,” she said with a grin. “Now. More shooting less talking? Does that sound good to you boys?”

“I guess,” John said. They stayed in the armory for another two hours, his weapons getting upgraded every few shots. Soon he was handling weapons he’d never seen before in his life, but with some instruction from Rory he was getting the hang of them pretty quickly. By the time they were done he was starting to get hungry again, and when they got back to the main room he saw lunch had arrived, in the form of Chinese take-out. They all dug in, and then Jack said he wanted John to start training Martha and Rory in combat medicine.

It had been a while since he’d done it, but he found the training was easily remembered and he managed to get through the basics. Since both of them had medical training it was easier and four hours had passed by the time he looked at a clock again. Jack told everyone except John to go home for the day and to be back at nine the next morning. The others collected their things and left leaving Jack and John alone. “Let’s get you set up in the system, so you can access all the stuff here,” Jack said. “Just fingerprints and a retina scan.”

“All right,” John said. They went to the door he had watched Amy open earlier, and Jack set things up. After they checked to make sure everything worked they went back inside and Jack handed him a folder. “What’s this?”

“Everything River had on Sherlock Holmes,” he said. “Apparently the time he disappeared after his confrontation with Moriarty are known as his lost years. No biographer figured out what he was doing or where he went, even though many tried. We know he pops up again sometime around a year from now, and that you are instrumental in bringing him home.”

“And afterwards?” John asked flipping through the file.

“To quote River, spoilers,” Jack said with a slight grin. “It’s not good to know too much about the future,, unless you’re a time traveler. But the good news is you find him and bring him home.” He clapped John on the shoulder. “Just remember that you work for Torchwood now and that comes before finding your friend.”

“All right,” John said with a nod. “Thank you for this.”

“No problem,” Jack said with a grin. “See you tomorrow at nine.” And with that, he turned and went towards what John assumed was his office, further into the building. John turned around and left, going back out into the alley and then heading home. He studied the file for a few hours as he ate leftovers for dinner,, and when he finally went to sleep that evening it seemed to be more restful. Perhaps this change was going to be for the best after all…

**Works inspired by this one:**

  * [Podfic: New Beginnings](https://archiveofourown.org/works/625917) by [AfroGeekGoddess](https://archiveofourown.org/users/AfroGeekGoddess/pseuds/AfroGeekGoddess)




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